Data
load("input/limma_SC_Controls.RData")
lab <- dea.limma
load("input/limma_SC_Controls_lit.RData")
lit <- dea.limma
logFC comparison
PND7/8 vs PND14/15
lab.fc.pnd <- lab$`PND8 vs PND15`[abs(lab$`PND8 vs PND15`$logFC) >= 1 & lab$`PND8 vs PND15`$adj.P.Val <= 0.05, ]
lab.fc.pnd1 <- lab.fc.pnd$logFC
names(lab.fc.pnd1) <- lab.fc.pnd$Genes
lit.fc.pnd <- lit$`PND7 vs PND14`[abs(lit$`PND7 vs PND14`$logFC) >= 1 & lit$`PND7 vs PND14`$adj.P.Val <= 0.05, ]
lit.fc.pnd1 <- lit.fc.pnd$logFC
names(lit.fc.pnd1) <- lit.fc.pnd$Genes
genes <- intersect(names(lab.fc.pnd1), names(lit.fc.pnd1))
fit <- lm(lit.fc.pnd1[genes] ~ lab.fc.pnd1[genes])
plot_ly() %>%
add_trace(x = lab.fc.pnd1[genes], y = lit.fc.pnd1[genes], mode = "markers") %>%
add_trace(x = lab.fc.pnd1[genes], y = predict(fit), mode = "lines") %>%
layout(
xaxis = list(title = "PND8 vs PND15 (Lab)"),
yaxis = list(title = "PND7 vs PND14 (Literature)"),
title = "SC controls logFC: Lab vs Literature"
)
PND14/15 vs Adult/PNW8
lab.fc <- lab$`PND15 vs Adult`[abs(lab$`PND15 vs Adult`$logFC) >= 1 & lab$`PND15 vs Adult`$adj.P.Val <= 0.05, ]
lab.fc1 <- lab.fc$logFC
names(lab.fc1) <- lab.fc$Genes
lit.fc <- lit$`PND14 vs Adult`[abs(lit$`PND14 vs Adult`$logFC) >= 1 & lit$`PND14 vs Adult`$adj.P.Val <= 0.05, ]
lit.fc1 <- lit.fc$logFC
names(lit.fc1) <- lit.fc$Genes
genes <- intersect(names(lab.fc1), names(lit.fc1))
fit <- lm(lit.fc1[genes] ~ lab.fc1[genes])
plot_ly() %>%
add_trace(x = lab.fc1[genes], y = lit.fc1[genes], mode = "markers") %>%
add_trace(x = lab.fc1[genes], y = predict(fit), mode = "lines") %>%
layout(
xaxis = list(title = "PND15 vs Adult (Lab)"),
yaxis = list(title = "PND14 vs PNW8 (Literature)"),
title = "SC controls logFC: Lab vs Literature"
)
SessionInfo
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.1 (2019-07-05)
## os Ubuntu 16.04.6 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Zurich
## date 2019-12-11
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
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## backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
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## callr 3.3.2 2019-09-22 [1] CRAN (R 3.6.1)
## cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
## colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
## crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
## crosstalk 1.0.0 2016-12-21 [1] CRAN (R 3.6.1)
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## fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
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## tidyr 1.0.0 2019-09-11 [1] CRAN (R 3.6.1)
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## vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
## viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.1)
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## zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
##
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## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library
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